Package that provides tools for brain MRI Deep Learning pre-processing.

Note

This page is a reference documentation. It only explains the function signature, and not how to use it. Please refer to the gallery for the big picture.

brainprep.spatial.bet2(imfile, brainfile, frac=0.5, cleanup=True, check_pkg_version=False)[source]¶

Skull stripped the MRI image.

Note

This function is based on FSL.

Parameters:

imfile : str

the input image.

brainfile : str

the path to the brain image file.

frac : float, default 0.5

fractional intensity threshold (0->1);smaller values give larger brain outline estimates

cleanup : bool, default True

optionnally add bias field & neck cleanup.

check_pkg_version : bool, default False

optionally check the package version using dpkg.

Returns:

brainfile, maskfile : str

the generated files.